Biology subjects

Pham, Q. D.

Publications and source records attributed to Pham, Q. D..

4 recordsLinked to original sources

bioRxiv2026

Influence of antibody-antigen interaction on fluorescence of Rhodamine 6G conjugated to the antibodies measured in human serum

Fluorescent dyes conjugated to monoclonal antibodies specifically trastuzumab (TRAS) and pertuzumab (PERT) serve as sensitive reporters of changes in the local energetic environment arising from antibody-antibody and antibody-antigen interactions. Upon covalent conjugation, the antibody local environment perturbates the energetic state of the dye, resulting in changes of the fluorescence emission energy and emission width of the dye. The dependence of these spectral parameters on antibody concentration was measured in HBS-8, diluted and undiluted human serum. In addition, the emission energy and emission width of dye-conjugated TRAS were investigated as a function of recombinant human epidermal growth factor receptor 2 (HER2) extracellular domain concentration in HBS-8 and in diluted and undiluted human serum. Antibody-antibody and antibody-antigen interactions produce remarkable contributions into the emission energy and emission width. These contributions depend on the composition of the surrounding medium. Our study showed that the samples containing 100 nM TRAS in serum exhibited the largest spectral changes upon interaction with HER2 suggesting that antibody-antigen interaction are not linear across concentration range of the antibodies. Moreover, our results demonstrate that interactions between dye-conjugated antibodies and their binding partners can be detected under physiologically relevant conditions. These findings establish fluorescence emission energy and emission width analysis as a potential approach for probing antibody interactions in complex biological matrices.

biophysics↗

bioRxiv2026

Cooperativity and Conformational Rearrangements in Protein-Protein and Protein-Ligand Interactions

Streptavidin-biotin, avidin-biotin interactions are classical models for protein-ligand binding, yet the energetic changes accompanying biotin binding remain poorly resolved. Using fluorescent dyes as energy sensors, we show that biotin binding produces two distinct regimes occurring in parallel as concentration of biotin increases cooperativity and conformational rearrangements, wherein cooperativity is observed via exchange broadening of fluorescence linewidth and conformational rearrangements exclusively observed in emission energy. Where the first biotin binding creates the highest contribution to the emission energy. Further analysis of tetramer-tetramer only interactions revealed extremely long ranged intermolecular interactions extending to hundreds of nm. The intermolecular interactions become negligible only at concentrations of approximately 10 nM for both streptavidin and avidin. Affinity values estimated for these diluted samples were below 1 nM.

biophysics↗

bioRxiv2024

In vitro disintegration of lozenge in oral cavity

The aim of this study is to develop a new in vitro disintegration method for lozenges in the oral cavity (OC) by mimicking physiologically relevant conditions in the OC including saliva flow rate and suction. Disintegration of solid-state dosage forms in the OC can be employed for local absorption in the OC or for delivering to the succeeding parts of the gastrointestinal tract. Understanding the disintegration is important before gaining insight into dissolution and absorption. Here abrasion force and rate exerted on the lozenge during the disintegration are controlled by a texture analyser. We showed that a higher flow rate and more frequent abrasion can lead to a faster disintegration, while variation of the compression force within a range in this study does not affect the disintegration statistically. The results are relevant to different types of consumers with variation in saliva production, for example, people with salivary dysfunction including elderly people. It is also important to consider these effects when formulating flavor and taste of lozenge that can affect consumer perception and consequently suction force and rate or saliva production. We could also observe disintegrated but not dissolved parts of the lozenge by using this apparatus, demonstrating the importance of the correlation between disintegration and dissolution when considering drug absorption in the OC to overcome the challenges of drug clearance from the OC by swallowing.

biophysics↗

bioRxiv2020

WHOLE-GENOME SEQUENCING AND DE NOVO ASSEMBLY OF A 2019 NOVEL CORONAVIRUS (SARS-COV-2) STRAIN ISOLATED IN VIETNAM

The pandemic COVID-19 caused by the zoonotic virus SARS-CoV-2 has devastated countries worldwide, infecting more than 4.5 million people and leading to more than 300,000 deaths. Whole genome sequencing (WGS) is an effective tool to monitor emerging strains and provide information for intervention, thus help to inform outbreak control decisions. Here, we reported the first effort to sequence and de novo assemble the whole genome of SARS-CoV-2 using PacBios SMRT sequencing technology in Vietnam. We also presented the annotation results and a brief analysis of the variants found in our SARS-CoV-2 strain, which was isolated from a Vietnamese patient. The sequencing was successfully completed and de novo assembled in less than 30 hours, resulting in one contig with no gap and a length of 29,766 bp. All detected variants as compared to the NCBI reference were highly accurate as confirmed by Sanger sequencing. The results have shown the potential of long read sequencing to provide high quality WGS data to support public health responses, and advance understanding of this and future pandemics.

genomics↗